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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Ventricular Morphometry Analysis System Resource Report Resource Website |
Ventricular Morphometry Analysis System (RRID:SCR_019007) | VMAS | data analysis software, data processing software, software application, software resource | Software tool to generate whole connected 3D brain ventricular shape model and encode ventricular surface deformation information that is inaccessible by ventricle volume measure. Contains automated segmentation approach and surface based multivariate morphometry statistics. | 3D brain model generation, 3D brain, ventricular shape model, ventricular surface deformation encoding, ventricle volume measure, automated segmentation, multivariate morphometry statistics, analysis system |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Arizona State University; Arizona; USA |
Free, Available for download, Freely available | http://gsl.lab.asu.edu/software/ventricle/ | SCR_019007 | SciCrunch Registry | 2026-10-10 12:40:23 | 0 | ||||||||
|
E-CRISP Resource Report Resource Website 100+ mentions |
E-CRISP (RRID:SCR_019088) | data access protocol, software resource, web service | Web application to design gRNA sequences. Uses algorithms to identify sgRNA target sequences in any nucleotide sequence for use in CRISPR/Cas mediated genome editing. Used for fast CRISPR target site identification. Enables designing of multiple libraries and creates genome scale libraries for several organisms in few hours. | gRNA sequence design, sgRNA target sequence identification, CRISPR, CRISPR/Cas mediated genome editing, library design, multiple libraries, genome scale libraries, bio.tools |
is listed by: Debian is listed by: bio.tools |
European Research Council Advanced Grant of the European Commission | PMID:24481216 | Free, Freely available | biotools:e-crisp | https://bio.tools/e-crisp | SCR_019088 | SciCrunch Registry | 2026-10-10 12:40:33 | 147 | ||||||
|
OpenCOR Resource Report Resource Website 1+ mentions |
OpenCOR (RRID:SCR_019001) | simulation software, software application, software resource | Open source cross platform modeling environment for reproducible science. Used to organise, edit, simulate and analyse models described in CellML format, using SED-ML and COMBINE archives. | Modeling environment, reproducible science, CellML format model, CellML format model analysis, CellML format model simulation |
uses: Simulation Experiment Description Markup Language is used by: SPARC Portal |
Free, Available for download, Freely available | SCR_019001 | SciCrunch Registry | 2026-10-10 12:40:23 | 6 | ||||||||||
|
datasets.datalad.org Resource Report Resource Website 1+ mentions |
datasets.datalad.org (RRID:SCR_019089) | data or information resource, data repository, data set, service resource, storage service resource | DataLad data distribution. Super dataset collating DataLad datasets from various sources including OpenNeuro, CRCNS, etc., to provide unified access to over 200TB of neural data. | Version control system, data distribution, super dataset, DataLad dataset, neural data | is related to: DataLad | NIBIB P41 EB019936; NSF 1429999; NSF 1912266 |
Free, Freely available | https://www.datalad.org/datasets.html | SCR_019089 | SciCrunch Registry | 2026-10-10 12:40:25 | 8 | ||||||||
|
HADDOCK Resource Report Resource Website 100+ mentions |
HADDOCK (RRID:SCR_019091) | data access protocol, simulation software, software application, software resource, web service | Software tool as information driven flexible docking approach for modeling of biomolecular complexes.User friendly integrative modeling of biomolecular complexes.HADDOCK v 2.2 offers new features such as support for mixed molecule types, additional experimental restraints and improved protocols, all of this in user friendly interface. | Molecular docking, data driven, biomolecular complex, grid computing, hybrid modeling, protein complex | has parent organization: Utrecht University; Utrecht; Netherlands | PMID:12580598 PMID:26410586 |
Restricted | https://www.bonvinlab.org/software/haddock2.2/, https://wenmr.science.uu.nl/haddock2.4/ | SCR_019091 | SciCrunch Registry | HADDOCK2.2, HADDOCK2.4, High Ambiguity Driven protein-protein DOCKing | 2026-10-10 12:40:25 | 168 | |||||||
|
EnteroBase Resource Report Resource Website 100+ mentions |
EnteroBase (RRID:SCR_019019) | data access protocol, data or information resource, database, software resource, web service | Integrated software environment that supports identification of global population structures within several bacterial genera that include pathogens. Web service for analyzing and visualizing genomic variation within bacteria. Genome database to enable to identify, analyse, quantify and visualise genomic variation within bacterial genera including Salmonella, Escherichia/Shigella, Clostridioides,Vibrio,Yersinia,Helicobacter,Moraxella. | Bacteria, pathogen, genome, Illumina short read, genotype, core genome multilocus, sequence typing, cgMLST, cgMLST sequence, bacterial strain mapping, visualizing genomic variation, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools has parent organization: University of Warwick; Coventry; United Kingdom |
Biotechnology and Biological Sciences Research Council ; Wellcome Trust |
Restricted | biotools:Enterobase | https://bio.tools/EnteroBase | SCR_019019 | SciCrunch Registry | 2026-10-10 12:40:24 | 317 | |||||||
|
D-GENIES Resource Report Resource Website 50+ mentions |
D-GENIES (RRID:SCR_018967) | alignment software, data processing software, image analysis software, software application, software resource, standalone software, web application | Open source software package developed in Python and JavaScript. Standalone and web application tool performing large genome alignments and generating interactive dot plots. Designed to compare two genomes. Used to sort query sequences along reference, zoom in plot and download several image, alignment or sequence files. Allows to display dot plots from other aligners by uploading their PAF or MAF alignment file. | bio.tools |
uses: Minimap2 is listed by: Debian is listed by: bio.tools |
PMID:29888139 | Free, Available for download, Freely available | biotools:d-genies | https://github.com/genotoul-bioinfo/dgenies, https://bio.tools/d-genies | SCR_018967 | SciCrunch Registry | Dot plot large GENomes in an Interactive, Efficient and Simple way | 2026-10-10 12:41:00 | 56 | ||||||
|
Hiroshima University Amphibian Research Center Resource Report Resource Website 10+ mentions |
Hiroshima University Amphibian Research Center (RRID:SCR_019015) | ARC, HUARC | biomaterial supply resource, material resource, organism supplier | Stock center that provides amphibian organisms, frogs and newts, primarily to Japanese investigators. The center runs the National BioResource Project (NBRP) Clawed frogs / Newts, which is financially supported by the Ministry of Education, Culture, Sports, Science and Technology (MEXT), Japan, to distribute these resources. Contributes to maintenance of biologically important strains of frogs and study biological characteristics of amphibian focusing genetics, developmental regulation, speciation, phylogeny, phenotype expression, and environment-induced mutagenesis. | Amphibian, Frog, Xenopus, Newt, Hiroshima University | Ministry of Education ; Culture ; Sports ; Science and Technology (MEXT) |
https://xenopus.nbrp.jp/NBRP_Xenopus/NBRP_X._tropicalis_Top_Page_EN.html | SCR_019015 | SciCrunch Registry | Amphibian Research Center, Institute for Amphibian Biology | 2026-10-10 12:40:23 | 10 | ||||||||
|
PROSPERO Resource Report Resource Website 1000+ mentions |
PROSPERO (RRID:SCR_019061) | data or information resource, database, narrative resource, standard specification | International database of prospectively registered systematic reviews in health and social care, welfare, public health, education, crime, justice, and international development, where there is health related outcome. Key features from review protocol are recorded and maintained as permanent record. Aims to provide comprehensive listing of systematic reviews registered at inception to help avoid duplication and reduce opportunity for reporting bias by enabling comparison of completed review with what was planned in protocol. | Gold standard authority, registered systematic reviews, reviews in health, reviews in social care, reviews in welfare, reviews in public health, reviews in education, reviews in crime, reviews in justice, reviews in international development, health related outcome, protocol, FASEB list |
is related to: Centre for Reviews and Dissemination has parent organization: University of York, York, England |
NIHR | Free, Freely available | SCR_019061 | SciCrunch Registry | 2026-10-10 12:40:24 | 3301 | |||||||||
|
Fgenesh plus plus Resource Report Resource Website 1+ mentions |
Fgenesh plus plus (RRID:SCR_018928) | simulation software, software application, software resource | Software tool as pipeline for automatic prediction of genes in eukaryotic genomes based on Softberry gene finding software. | Automatic gene prediction, eukaryotic genomes, Softberry software, gene finding | is related to: FGENESH Plus | PMID:16925832 | Restricted | SCR_018928 | SciCrunch Registry | Fgenesh Plus Plus, FGENESH plus plus, FGENESH Plus Plus | 2026-10-10 12:40:29 | 7 | ||||||||
|
Long Ranger Resource Report Resource Website 10+ mentions |
Long Ranger (RRID:SCR_018925) | data analysis software, data processing software, software application, software resource, software toolkit | Software tool as set of analysis pipelines that processes Chromium sequencing output to align reads and call and phase SNPs, indels, and structural variants by 10x Genomics. | Analysis pipelines, process chromium sequencing output, align reads, call SNPs, phase SNPs, indel, structural variant, 10x Genomics | Restricted | SCR_018925 | SciCrunch Registry | 2026-10-10 12:40:22 | 14 | |||||||||||
|
ELDA Resource Report Resource Website 100+ mentions |
ELDA (RRID:SCR_018933) | analysis service resource, data analysis software, data processing software, production service resource, service resource, software application, software resource | Software tool for limiting dilution analysis, with particular attention to needs of stem cell assays. Provides confidence intervals for all LDA data sets, including those with 0% or 100% responses. Other features include test of adequacy of single hit hypothesis, tests for frequency differences between multiple data sets, and ability to take advantage of cases where number of cells in sample is counted exactly. | Limiting dilution analysis, stem cell assay, data set confidence intervals, single hit hypothesis, adequacy test, frequency differences test | is listed by: SoftCite | PMID:19567251 | Free, Freely available | SCR_018933 | SciCrunch Registry | Extreme Limiting Dilution Analysis | 2026-10-10 12:40:30 | 463 | ||||||||
|
Trinotate Resource Report Resource Website 10+ mentions |
Trinotate (RRID:SCR_018930) | data analysis software, data processing software, software application, software resource, software toolkit | Software annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. | Automatic functional annotation, transcriptome annotation, de novo assembled transcriptome, model organism, non model organism | Free, Available for download, Freely available | SCR_018930 | SciCrunch Registry | Transcriptome Functional Annotation and Analysis | 2026-10-10 12:40:22 | 37 | ||||||||||
|
Scayle Resource Report Resource Website |
Scayle (RRID:SCR_019064) | atlas, data or information resource, data repository, data set, portal, service resource, spatially referenced dataset, storage service resource | Open source data platform and multidisciplinary online repository where research groups and different organizations store and make public their datasets, managed by Scayle. Collection of public datasets are available through open.scayle.es and can be reused. NetFlow is network protocol developed by Cisco for collection and monitoring of network traffic flow data generated. Netflow datasets have been used to train machine learning models. | Netflow, DOROTHEA, dataset, network traffic, port scan, training data, traffic flow data | has parent organization: University of Leon, Spain | Free, Freely available, Available for download | https://open.scayle.es/dataset, https://open.scayle.es/dataset/netflow-data-with-sampling-for-test, https://open.scayle.es/dataset/netflow-data-with-sampling-for-training | https://open.scayle.es/dataset/netflow-data, https://open.scayle.es/dataset/netflow-data-without-sampling | SCR_019064 | SciCrunch Registry | open.scayle.es | 2026-10-10 12:41:01 | 0 | |||||||
|
University of Leon, Spain Resource Report Resource Website |
University of Leon, Spain (RRID:SCR_019071) | data or information resource, portal, topical portal | Spanish public university with campus in Leon and Ponferrada. | is parent organization of: Scayle | SCR_019071 | SciCrunch Registry | 2026-10-10 12:40:32 | 0 | ||||||||||||
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RAPIDO Resource Report Resource Website 1+ mentions |
RAPIDO (RRID:SCR_018935) | alignment software, data access protocol, data processing software, image analysis software, software application, software resource, web service | Web server for alignment of protein structures in presence of conformational changes. Used for 3D alignment of crystal structures of different protein molecules in presence of conformational change. Can identify structurally equivalent regions also when distant in terms of sequence and separated by other movable domains. | Protein structure alignment, rapid alignment, protein domain, conformational changes presence, 3D alignment, crystal structure, protein molecule, conformational change presence, identify structural region, distant sequence, movable domains | Associazione Italiana per la Ricerca sul Cancro ; European Molecular Biology Laboratory |
PMID:18460546 PMID:18727838 |
Free, Freely available | SCR_018935 | SciCrunch Registry | Rapid Alignment of Proteins in terms of Domains, Rapid alignment of proteins in terms of domains | 2026-10-10 12:40:22 | 2 | ||||||||
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UCSC Xena Resource Report Resource Website 1000+ mentions |
UCSC Xena (RRID:SCR_018938) | analysis service resource, data access protocol, data or information resource, portal, production service resource, service resource, software resource, web service | Web tool where one component is front end Xena Browser and another component is back end Xena Hubs. Web based Xena Browser empowers biologists to explore data across multiple Xena Hubs with variety of visualizations and analyses. Xena Hubs host genomics data from laptops, public servers, behind firewall, or in cloud, and can be public or private. Xena Browser receives data simultaneously from multiple Xena Hubs and integrates them into single coherent visualization within browser. Allows users to explore functional genomic data sets for correlations between genomic and/or phenotypic variables. | Data visualization, data analysis, genomics data, explore functional genomic data, functional genomic, data sets, genomic variable correlation, phenotypic variables correlation | has parent organization: University of California at Santa Cruz; California; USA | Free, Freely available | https://xenabrowser.net/ | SCR_018938 | SciCrunch Registry | UCSC Xena Browser, Xena Browser | 2026-10-10 12:40:22 | 4804 | ||||||||
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o²S²PARC Resource Report Resource Website 1+ mentions |
o²S²PARC (RRID:SCR_018997) | osparc | simulation software, software application, software resource | Simulation platform that enables users to create, access, tune, and run models or computational algorithms through web based interface. Web interactive simulation platform that hosts SPARC computational models and solvers. Allows collaborative development and sharing, model coupling and cloud based execution, data visualization and analysis, and ensures sustainability of computational models developed within SPARC. Enables users to create predictive, multiscale, multi-physics models spanning from modulation sources acting on peripheral nervous system (PNS) to resulting modulation of organ functional response. | SPARC, SPARC computational model, data sharing, model coupling, cloud based execution, data visualization, data analysis, peripheral nervous system, organ functional response |
is used by: SPARC Portal is organization facet of: SPARC Portal |
Free, Freely available | SCR_018997 | SciCrunch Registry | open online Simulation platform for Stimulating Peripheral Activity to Relieve Conditions | 2026-10-10 12:40:31 | 2 | ||||||||
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Protein.Plus Resource Report Resource Website 50+ mentions |
Protein.Plus (RRID:SCR_019044) | data access protocol, software resource, web service | Web server is focused on protein ligand interactions. Provides support for initial steps when dealing with protein structures, namely structure search, quality assessment, and preprocessing. Furthermore, advanced options, such as protein pocket detection, ensemble generation or prediction of metal coordinations are supported. | Protein ligand interaction, protein structure, quality assessment, protein pocket detection, ensemble generation, metal coordinations prediction | has parent organization: University of Hamburg; Hamburg; Germany | Free, Freely available | SCR_019044 | SciCrunch Registry | 2026-10-10 12:40:32 | 59 | ||||||||||
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fracridge Resource Report Resource Website 1+ mentions |
fracridge (RRID:SCR_019045) | 1d time-series analysis software, data analysis software, data processing software, software application, software resource, time-series analysis software | Software tool as regularization technique that penalizes L2-norm of coefficients in linear regression. Available in two programming languages MATLAB and Python. | Generalized linear model, hyperparameters, regularization technique, coefficient, linear regression, L2 norm, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:fracridge | https://bio.tools/fracridge | SCR_019045 | SciCrunch Registry | fractional ridge regression | 2026-10-10 12:40:24 | 1 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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